BLUE
Profile banner
KH
Kat Holt
@katholt.bsky.social
Scientist… pathogen genomics & antimicrobial resistance, computational biology & infectious disease epi. Co-Director LSHTM AMR Centre. Academic Editor PLoS Biology. holtlab.net | klebnet.org | typhoidgenomics.org | amr.lshtm.ac.uk
402 followers139 following35 posts
KHkatholt.bsky.social

Authors - post a description of the software, Nature - write a news feature covering this… dressing it up with the veneer of a peer reviewed article is a damaging farce. Submit for peer review when you’re ACTUALLY READY to be reviewed.

0
KHkatholt.bsky.social

Fundamentally, if the journal is not actually peer reviewing the software, what is the point of them publishing an article describing it? Answer: Advertising (for the authors) and citations (for the journal). None of this lives up to the purpose or standards of scholarly publishing.

1
Reposted by Kat Holt
MHmichaelhoffman.bsky.social

I'm going to translate their editorial into English: It's important to note that we at Nature have really high standards for materials, data, and code sharing, which we will enforce assiduously for plebes. But do remember that while all authors are equal, some are more equal than others.

But why allow the complete data and code to be restricted at the time of publication? Nature’s editorial policies have been developed to support open science and state: “Authors are required to make materials, data, code, and associated protocols promptly available to readers without undue qualifications.” One way we enable researchers to do so is through a partnership with Code Ocean, a computational-science platform that makes the information reproducible and traceable. But our policies also acknowledge that there can be restrictions, which “must be disclosed to the editors at the time of submission” and agreed with editors. The policy also states: “Any reason that would preclude the need for code or algorithm sharing will be evaluated by the editors who reserve the right to decline the paper if important code is unavailable.”
2
KHkatholt.bsky.social

If you know a lot about AMR mechanisms in a bacterial pathogen, consider joining us in ESGEM-AMR to share your expertise and develop #AMRrulesbit.ly/AMRrules

0
KHkatholt.bsky.social

ESGEM, the ESCMID Study Group on Epidemiological Markers is launching a working group to develop standards for interpreting AMR genotypes. Much like EUCAST guidance for interpreting lab phenotypes as S/I/R, we want to define the AMRrules for interpreting genotypes.

1
Reposted by Kat Holt
WMwtmatlock.bsky.social

Very excited to announce our transdisciplinary AMR workshop 🎉 Join us to hear perspectives and discussion from patient activists, journalists, philosophers, microbiologists, historians, clinicians, policy makers, and artists. More info: www.torch.ox.ac.uk/event/commun...

A poster for a workshop called “Communication, Narratives, and Antimicrobial Resistance”. 9am to 6pm 16th May 2024. Merton College, University of Oxford.
1
Reposted by Kat Holt
SOsiderophile.bsky.social

Our dept at Trinity College Dublin is looking for a Tenure-Track Assistant Professor! Details below 👇 www.jobs.ac.uk/job/DGO006/a...

0
Reposted by Kat Holt
KJkjolley.bsky.social

New preprint out now - stable bacterial strain nomenclature with Life Identification Numbers using a gene-by-gene approach. From our wonderful collaborators at the Institut Pasteur. www.biorxiv.org/content/10.1...

Bacterial strain nomenclature in the genomic era: Life Identification Numbers using a gene-by-gene approach
Bacterial strain nomenclature in the genomic era: Life Identification Numbers using a gene-by-gene approach

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

1
Reposted by Kat Holt
PAflashton.bsky.social

How does the ONT R.10.4.1 yield compare with R.9.4.1. I remember seeing some data from ages ago that showed that R.10 yield was lower. Still true?

5
Profile banner
KH
Kat Holt
@katholt.bsky.social
Scientist… pathogen genomics & antimicrobial resistance, computational biology & infectious disease epi. Co-Director LSHTM AMR Centre. Academic Editor PLoS Biology. holtlab.net | klebnet.org | typhoidgenomics.org | amr.lshtm.ac.uk
402 followers139 following35 posts